How do I batch render multiple scenes with animation settings?
You can use a file output node in the compositor to save the renders from each scene to individual files. While multiple render layer nodes can trigger multiple scenes to be rendered, blender doesn't save each scene to file unless you connect it to a file output node.



For each render layer node a different scene can be selected as well as a render layer from that scene. Any number of inputs can be added to the file output node with each input having different filename settings and can use a different image format if desired.

The base path and the file subpath will be combined for each connection, a file subpath with a / will create subdirectories in the base path for the connection. If you want to use multiple base paths then you can add multiple file output nodes.

Now when you render this scene, the scene listed in each render layer will also get rendered and the connections to the file output node will all be saved to file.

As you have already setup multiple scenes you can use a script to create the master scene for rendering. This script should do most of the work.